[Vegan-commits] r1864 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 20 20:09:15 CEST 2011
Author: jarioksa
Date: 2011-09-20 20:09:15 +0200 (Tue, 20 Sep 2011)
New Revision: 1864
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-09-20 18:04:39 UTC (rev 1863)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-09-20 18:09:15 UTC (rev 1864)
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.1-0
+This is vegan 2.1-1
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x10221d350>
+<environment: 0x102618468>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -1830,6 +1830,96 @@
>
>
> cleanEx()
+> nameEx("commsim")
+> ### * commsim
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: commsim
+> ### Title: Create a Object for Null Model Algorithms
+> ### Aliases: commsim make.commsim print.commsim
+> ### Keywords: multivariate datagen
+>
+> ### ** Examples
+>
+> ## write the r00 algorithm
+> f <- function(x, n, ...)
++ array(replicate(n, sample(x)), c(dim(x), n))
+> (cs <- commsim("r00", fun=f, binary=TRUE,
++ isSeq=FALSE, mode="integer"))
+An object of class "commsim"
+"r00" method (binary, non-sequential, integer mode)
+
+>
+> ## retrieving the sequential swap algorithm
+> make.commsim("swap")
+An object of class "commsim"
+"swap" method (binary, sequential, integer mode)
+
+>
+> ## structural constraints
+> diagfun <- function(x, y) {
++ c(sum = sum(y) == sum(x),
++ fill = sum(y > 0) == sum(x > 0),
++ rowSums = all(rowSums(y) == rowSums(x)),
++ colSums = all(colSums(y) == colSums(x)),
++ rowFreq = all(rowSums(y > 0) == rowSums(x > 0)),
++ colFreq = all(colSums(y > 0) == colSums(x > 0)))
++ }
+> evalfun <- function(meth, x, n) {
++ m <- nullmodel(x, meth)
++ y <- simulate(m, nsim=n)
++ out <- rowMeans(sapply(1:dim(y)[3],
++ function(i) diagfun(attr(y, "data"), y[,,i])))
++ z <- as.numeric(c(attr(y, "binary"), attr(y, "isSeq")))
++ names(z) <- c("binary", "isSeq")
++ c(z, out)
++ }
+> x <- matrix(rbinom(10*12, 1, 0.5)*rpois(10*12, 3), 12, 10)
+> a <- t(sapply(c("r00","r0","r1","r2","c0",
++ "swap","tswap","quasiswap","backtrack",
++ "r2dtable","swap_count","quasiswap_count",
++ "swsh_samp","swsh_both","abuswap_r","abuswap_c",
++ "swsh_samp_r","swsh_samp_c","swsh_both_r","swsh_both_c",
++ "r00_ind","r0_ind","c0_ind",
++ "r00_samp","r0_samp","c0_samp",
++ "r00_both","r0_both","c0_both"),
++ evalfun, x=x, n=10))
+> print(as.table(ifelse(a==1,1,0)), zero.print = ".")
+ binary isSeq sum fill rowSums colSums rowFreq colFreq
+r00 1 . 1 1 . . . .
+r0 1 . 1 1 1 . 1 .
+r1 1 . 1 1 1 . 1 .
+r2 1 . 1 1 1 . 1 .
+c0 1 . 1 1 . 1 . 1
+swap 1 1 1 1 1 1 1 1
+tswap 1 1 1 1 1 1 1 1
+quasiswap 1 . 1 1 1 1 1 1
+backtrack 1 . 1 1 1 1 1 1
+r2dtable . . 1 . 1 1 . .
+swap_count . 1 1 1 1 1 1 1
+quasiswap_count . . 1 1 1 1 . .
+swsh_samp . . 1 1 . . 1 1
+swsh_both . . 1 1 . . 1 1
+abuswap_r . 1 1 1 1 1 1 1
+abuswap_c . 1 1 1 1 1 1 1
+swsh_samp_r . . 1 1 1 . 1 1
+swsh_samp_c . . 1 1 . 1 1 1
+swsh_both_r . . 1 1 1 . 1 1
+swsh_both_c . . 1 1 . 1 1 1
+r00_ind . . 1 . . . . .
+r0_ind . . 1 . 1 . . .
+c0_ind . . 1 . . 1 . .
+r00_samp . . 1 1 . . . .
+r0_samp . . 1 1 1 . 1 .
+c0_samp . . 1 1 . 1 . 1
+r00_both . . 1 1 . . . .
+r0_both . . 1 1 1 . 1 .
+c0_both . . 1 1 . 1 . 1
+>
+>
+>
+> cleanEx()
> nameEx("contribdiv")
> ### * contribdiv
>
@@ -4085,6 +4175,97 @@
>
>
> cleanEx()
+> nameEx("nullmodel")
+> ### * nullmodel
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: nullmodel
+> ### Title: Null Model and Simulation
+> ### Aliases: nullmodel print.nullmodel simulate.nullmodel update.nullmodel
+> ### print.simmat
+> ### Keywords: multivariate datagen
+>
+> ### ** Examples
+>
+> x <- matrix(rbinom(10*12, 1, 0.5)*rpois(10*12, 3), 12, 10)
+>
+> ## non-sequential nullmodel
+> (nm <- nullmodel(x, "r00"))
+An object of class "nullmodel"
+"r00" method (binary, non-sequential)
+12 x 10 matrix
+
+> (sm <- simulate(nm, nsim=10))
+An object of class "simmat"
+"r00" method (binary, non-sequential)
+12 x 10 matrix
+Number of permuted matrices = 10
+
+>
+> ## sequential nullmodel
+> (nm <- nullmodel(x, "swap"))
+An object of class "nullmodel"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Iterations = 0
+
+> (sm1 <- simulate(nm, nsim=10, thin=5))
+An object of class "simmat"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Number of permuted matrices = 10
+Start = 1, End = 50, Thin = 5
+
+> (sm2 <- simulate(nm, nsim=10, thin=5))
+An object of class "simmat"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Number of permuted matrices = 10
+Start = 51, End = 100, Thin = 5
+
+>
+> ## sequential nullmodel with burnin and extra updating
+> (nm <- nullmodel(x, "swap"))
+An object of class "nullmodel"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Iterations = 0
+
+> (sm1 <- simulate(nm, burnin=10, nsim=10, thin=5))
+An object of class "simmat"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Number of permuted matrices = 10
+Start = 11, End = 60, Thin = 5
+
+> (sm2 <- simulate(nm, nsim=10, thin=5))
+An object of class "simmat"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Number of permuted matrices = 10
+Start = 61, End = 110, Thin = 5
+
+>
+> ## sequential nullmodel with separate initial burnin
+> (nm <- nullmodel(x, "swap"))
+An object of class "nullmodel"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Iterations = 0
+
+> update(nm, nsim=10)
+> (sm2 <- simulate(nm, nsim=10, thin=5))
+An object of class "simmat"
+"swap" method (binary, sequential)
+12 x 10 matrix
+Number of permuted matrices = 10
+Start = 11, End = 60, Thin = 5
+
+>
+>
+>
+> cleanEx()
> nameEx("oecosimu")
> ### * oecosimu
>
@@ -4819,7 +5000,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106d76540>
+<environment: 0x106cb7ab0>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4835,7 +5016,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x105526dc8>
+<environment: 0x105071788>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4991,7 +5172,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106aa0b90>
+<environment: 0x106225ae0>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -5004,7 +5185,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106b79758>
+<environment: 0x1078e2f58>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -5017,7 +5198,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106d64b80>
+<environment: 0x107e70e00>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -7277,7 +7458,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106f7e208>
+<environment: 0x107d87dc8>
Estimated degrees of freedom:
2 total = 3
@@ -7753,7 +7934,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 159.371 1.809 164.032 0 0
+Time elapsed: 111.738 1.253 113.941 0 0
> grDevices::dev.off()
null device
1
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